I’ve created this structure that is essentially a cube with hexagons subtracted from each face. I had no issues subtracting the hexagons from two faces, however on the last face I am only able to subtract certain hexagons.

Selecting the subtract option just defaults back to whichever extrusion profile was previously set. I’ve tried many different troubleshooting steps but can’t seem to get it to work. Please help!

Welcome to the forum @jbeck !
I’m not sure of how you constructed each side but try creating one side and then duplicating it.
Here is a rough example.

Hi,
the problem you encounter comes from the fact you are working on a solid cube, and by doing the subtraction on 3 faces, you create very complex inner geometry, with very thin surfaces and sharp edges that are problematic.
Here are 2 cuts view to illustrate the issue and to show how complex the geometry is.

So, in the solution suggested by @WORTHYimage you don’t have these problem because the inner of the cube is empty. If it is OK, then this is the best solution as it creates simple geometry.

If you absolutely need to work on a solid cube, there is a workaround: for the face that is problematic, proceed in two steps:

extrude the hexagons only a small distance

then select the hexagon and use offset face
This will take some computing time but you should succeed.